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Research ArticleISSN 2637-4609
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent
Jeel Moya-Salazar12 Joaquiacuten Veacutertiz-Osores3 Sandro Jibaja4 Romaacuten Acevedo-Espinola5 Rocioacute Rupa2 Mitchell Alarcoacuten-Diacuteaz3 Miluska Vega-Guevara6 and Robert Cucho- Flores7
1Hospital Nacional Docente Madre Nintildeo San Bartolomeacute Peru
2Facultad de Ciencias y Filosofiacutea Universidad Peruana Cayetano Heredia Peru
3Escuela de posgrado Universidad Ceacutesar Vallejo Peru
4Universidad Ricardo Palma Peru
5Facultad de Ciencias de la Salud Universidad Privada Norbert Wiener Peru
6Escuela de Posgrado Universidad Marcelino Champagnat Peru
7Universidad Alas Peruanas Peru
Corresponding author Jeel Moya-Salazar Facultad de Ciencias y Filosofiacutea Universidad Peruana Cayetano Heredia Hospital Nacional Docente Madre Nintildeo San Bartolomeacute Lima Peru
Received January 25 2019 Published June 18 2019
Abstract
Lipases are enzymes that catalyze the hydrolysis of long chain triglycerides These enzymes have a key role in several human practices and industries and it has been used in bioremediation processes Due to the stability and specificity to their substrates under various conditions their interest has grown during the last decade The effluent from the palm oil industry contains about ~44 saturated fatty acids (mainly palmitic) ~37 monounsaturated fatty acids (mainly oleic acid) and 10 polyunsaturated fatty acids potentially dangerous for the ecosystem Bacteria and fungi contain lipases that are capable of degrade these lipids but there are no sufficient studies on how these enzyme interacts with their substrates In this study by homology modeling lipases 3D structure of Mucor circinelloides f circinelloides 1006PhL and Rhizopus oryzae strains were modeled in silico using the SWISS-MODEL server The best models with stable structures were verified using the tool PROCHECK and Errat Server model Further a molecular docking was carried out between the selected modeled 3D structures with linoleic linolenic oleic palmitic acid and tripalmitin using SwissDock tool to predict the lower binding energy of these lipases Furthermore the molecular docking analysis of 3D models of lipases from Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases
IntroductionSoil fungi are important for a wide variety of industrial
processes The use of fungi is based on their ability to produce enzymes of industrial interest such as lipases that are widely used in the treatment of effluents To date the genera Mucor Rhizopus Penicillium and Aspergillus have been tested with potential use in bioremediation [1-3]
Lipases (EC 3113) a subclass of esterases reversibly catalyze the hydrolysis of long-chain triglycerides [4] It has recently been shown that fungal lipases display levels of activity and stability in non-aqueous environments This remarkable feature facilitates esterification and transesterification [5] Usually lipid-specific reactions can be produced with high performance from fungi without requiring cofactors In the case of bioremediation these
DOI 1032474AOICS201904000182
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
enzymes have been used for degradation of palm oil effluent [16-8]
In silico methods helps in the predictions of enzymatic affinity activity specificity and selectivity of newly discovered proteins from structure information [9] For example molecular docking methods have also been applied successfully to predict most likely enzyme substrates with unknown experimental molecular interaction to its substrate [10] This kind of bioinformatics approaches allow the previous screening of potential target for application in bioremediation and take advantage of fungi enzymes for industrial applications
This method of predicting the enzyme-substrate complex structure can be accomplished through two unified steps first by sampling conformations of the ligand (eg fatty acids tripalmitin etc) in the active site of the protein and second by classifying these conformations by a score that ranks most negative value among all the conformations generated which indicates greater stability [11] Molecular docking studies could help to identify pollutants fatty acids suitable to be degraded by these enzymes [12]
Although it has been reported amino acid sequences of lipases from bacteria and fungi with these properties tested in vitro [13] their crystal structure in Protein Data Bank has not yet been reported Hence our study is focused on predicting the 3D structure by homology modeling from lipase amino acids sequences of Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] and subsequently the interaction of modeled structures with fatty acids and tripalmitin were analyzed by molecular docking for calculating the full fitness energy (Kcalmol)
Materials and MethodsFungi sequence selection and alignment
The amino acid sequence of the reference lipase of Rhizopus microsporus var Chinensis [EF405962] and the target amino acid sequences Mucor circinelloides f circinelloides 1006PhL [EPB86304] and R oryzae [AER14043] were obtained from
Genbank (httpwwwncbinlmnihgovgenbank) We assessed whether all had registered their 3D structure UniProt (httpwwwuniprotorguniprot) and PDB (httpwwwrcsborgpdbhomehomedo) databases We inspected and adjusted manually the sequences using the software BioEdit v725 to diminish the number of gaps and insertions Then the alignment was performed with ClustalW2 and with PROSITE online tool (httpprositeexpasyorg) was determined the corresponding active site in PROSITE tool [14]
Homology modeling
The templates crystal structures were retrieved from RCSB Protein Data Bank (PDB) in base to identity (gt30) We did the homology modeling with SWISSMODEL (httpswissmodelexpasyorginteractive) which is a fully automated protein structure homology-modeling server accessible via the ExPASy web server [15] The process considered the following steps
(i) Template identification
(ii) Template selection
(iii) Model building and
(iv) Model quality estimation
The modeled structures were further verified with programs such as PROCHEK which Checks stereochemical quality of protein structures [16] and Errat (httpwwwdoe- mbiuclaeduServicesErrathtml)
Molecular dockingMolecular docking was performed SwissDock server (http
wwwswissdockchdocking) to decipher the binding affinity and mode of interaction of the selected compounds (Scheme 1) against fungi lipases (of interest) SwissDock requires the target protein and ligand in PDB and Mol2 format respectively The ligands specified in Figure 1 As described by Grosdidier et al [17] SwissDock is based on the docking software EADock DSS whose algorithm consists of the following steps
Figure 1 Chemical structures of ligands used for molecular docking (A) Linoleic acid [PubChem 4474613] (B) linolenic acid [PubChem 5280934] (C) linolenic acid [PubChem 3802189] (D) Oleic acid [PubChem 6845860] (E) Palmitic acid [PubChem 6072466] and (F) Tripalmitin [PubChem 8214701]
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
1 Binding modes are generated either in a box (local docking) or near all target cavities (blind docking)
2 Simultaneously CHARMM energies of the binding modes are estimated on a grid
3 The binding modes with most favorable energies are evaluated with FACTS and clustered
4 Most favorable clusters are visualized online and downloaded and the obtained dock scores are reported in kcalmol [17]
We analyzed docking results thru the UCSF Chimera program (RBVI US) which provides an insight into the molecule to observe it specifically at the atomic level
Results and DiscussionThe amino acids sequences of the template and the query
lipases were aligned with Clustal (Figure 2) The query sequences of Rhizopus oryzae [AER14043] and Mucor circinelloides f circinelloides 1006PhL [EPB86304 M circinelloides] consist of 294
and 360 residues respectively but the template structure was 389 residues Manual editing query sequences were modeled from all its length and after alignment the sequence identity was 6306 for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and 7959 for Rhizopus oryzae [AER14043] respect to the sequence template Rhizopus microsporus var Chinensis [EF405962] We employed the result of alignment as criteria to build 3D structures for both query sequences by homology modeling
Lipases are extensively distributed in prokaryotes and eukaryotes Most conserved region in all these proteins focuses on a serine residue [1819] with a residue of aspartic acid and a histidine in a charge relay system Blow (1990) demonstrated their interaction and participation in a charge relay system [20] Accordingly with PROSITE our models have a serine active site VIVTGHSLGG specific for lipase but Mucor circinelloides f circinelloides 1006PhL [EPB86304] lipase model differs by one amino acid respect to the template protein (a valine replaced Isoleucine) The conserved histidine and aspartic acid residues must be highlighted in Figure 2
Figure 2 Multiple alignments of amino acidic sequences of lipases from Rhizopus microsporus var Chinensis [EF405962 Rh microspoorus] and the target amino acid sequences Mucor circinelloides f circinelloides 1006PhL [EPB86304 M circinelloides] and Rhizopus oryzae [AER14043 Rh oryzae] performed with ClustalW2 Inside the box the active site amino acids specific for lipases are shown (VIVTGHSLGG)
Several studies suggest the broad and interesting use of the study with an in silico approach Habitually they are used in the modern designs of drug to comprehend the mechanisms of pharmacological interaction at the molecular level recognizing the network and the signaling pathways of genes and the substrate-enzyme interactions Due to the great development of the in silico studies it is that the computational approaches can intensely support and help to decipher these specifics interactions between lipases and triglycerides [21] The major objective of this study was to identify the binding energy of common pollutants fatty acids
and tripalmitin present in palm oil effluents Protein structure homology modeling has become a routine technique to generate 3D models for proteins when experimental structures are unavailable The improved SWISS-MODEL pipeline makes extensive use of model quality estimation to select of most suitable templates and provides estimates of the expected accuracy of the resulting models [22]
A newly developed interactive web interface allows us to suitably search for appropriate templates using sensitive Hidden Markov
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Models searches against the SWISS-MODEL Template Library analyses alternative templates and alignments perform structural superposition and comparison and compare the resulting models using mean force potential based model quality estimation tools Model quality estimation is an essential part of protein structure predictions as the accuracy of a model determines its usefulness for practical applications [22] By the structure of lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] has not been crystallized yet here the 3D structure of the lipase was predicted by homology modeling for both species favored by the high identity respect to its template
We selected the best model among three 3D models generated after the verification of all parameters (Figure 3 amp 4) Model quality declines with decreasing sequence identity A typical model has ~1ndash2Aring root mean square deviation between the matched Cα atoms at 70 sequence identity but only 2ndash4Aring agreement at 25 sequence identity However the errors are significantly higher in the loop regions where the amino acid sequences of the target and template proteins may be completely different [23] Our Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] models have 028Aring and 007Aring root mean square deviations between the matched Cα atoms with respect to template structure respectively
Figure 3 Errat plots of modeled lipases from Mucor circinelloides f circinelloides 1006PhL (upper) [EPB86304] and Rhizopus oryzae (bottom) [AER14043] The error values for model residues as predicted by ERRAT are shown The ldquoyrdquo axis presents the error value and ldquoxrdquo axis presents the amino acid sequences of lipase An error value exceeding 99 confidence level indicates poorly modeled regions
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Figure 4 (A) The Ramachandran plot of modeled protein of Mucor circinelloides f circinelloides 1006PhL [EPB86304] (left) showing 895 of the atom residing in the most favored region 96 in the allowed region 22 in the generously allowed region and 04 residues was in the disallowed region (B) The Ramachandran plot of modeled protein of Rhizopus oryzae [AER14043] (right) showing 897 of the atom residing in the most favored region 86 in allowed region 22 in generously allowed region and 04 residues was in disallowed region
The quality of the modeled structures was first analyzed with PROCHECK by Ramachandran plots We would be expected to have a good quality model over 90 in most favored regions based on an analysis of a resolution of at least 20Aring Angstroms and R-factor of ~20
The Ramachandran plot obtained from PROCHECK program with the Mucor circinelloides f circinelloides 1006PhL [EPB86304]
lipase model showed that 896 of residues were in most favored regions 96 residues were in additional allowed regions 13 in the generously allowed regions and 04 in the disallowed regions Likewise in the same way we validated the Rhizopus oryzae [AER14043] lipase model with 897 of total residues in most favored regions 86 residues in additional allowed regions 04 in the generously allowed and disallowed regions (Figure 5)
Figure 5 (A) Oleic acid molecule binds to Rhizopus oryzae modeled lipase 3D structure into the funnel form active site (-799 estimated ΔG) (B) Mucor circinelloides f circinelloides 1006PhL modelled lipase interacts with Palmitic acid (-645 estimated ΔG) (C) Tripalmitin binds to Rhizopus oryzae modeled lipase (-942 estimated ΔG)
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
We also used ERRAT (httpnihservermbiuclaedu) which analyses the statistics of non-bonded interactions between different atom types A single output plot was produced by Errat program that gave the value of the error function against position of residues [24] An error value exceeding 99 confidence level indicates poorly modeled regions (Figure 3) Errat analyses also provide an overall quality factor expressed as the percentage of the protein for which the calculated error value falls below the 95 rejection limit Good high resolution structures generally produce values around 95 or higher For lower resolutions (25ndash3Aring) the average overall quality factor is around 91 [24] The overall quality factor assigned for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase models were 883 and 934 respectively
Accordingly with docking study published here it was predicted that modeled lipases have most effective interaction with tripalmitin (binding energy of -957Kcalmol) Docking analysis of Mucor circinelloides f circinelloides 1006PhL modeled lipase with fatty acids and tripalmitin was performed and full fitness energy was recorded The results showed a good interaction more than
one-fatty acids and tripalmiting them (Table 1) We performed the docking with SwissDock with rigid selection We conducted the same procedure with Rhizopus oryzae modelled lipase with these substrates under the same parameters and software and the results were appropriate scores for binding
As a reference a Rhizopus microsporus var Chinensis [EF405962] lipase with PDB ID 4L3W was taken for comparison where accordingly with previous reports [1825-27] We recognized that the triad ArgndashAspndashPro (RDP) is preserved in the lipase responsible for the detection of the molecules tested Our data revealed the above mentioned (VIVTGHSLGG) conserved domain in the lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] as the main site for lipase activity We also observed that fatty acids and tripalmitin binds into the pocket of the funnel shape active site of both lipases and bonding between the molecules is through hydrogen bond with bond length ~250Aring as previously reported with another ligandenzyme [15] In contrast when we analyzed the result in the lipase the docking score was favorable and fatty acid and tripalmitin molecule were bind given to the protein low fullfitness energy (Table 1)
Table 1 Molecular docking scores for target lipase structures and possible substrates found in palm oil
Source of lipase Ligand Full Fitness (Kcalmol) Estimated ∆G (kJmol)
Rhizopus microspona var Chinensis [PDB 4L3W] ()
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-96678
-105211
-112517
-106898
-114375
-108237
-626
-752
-65
-62
-804
-837
Mucor circinelloides f circinelioides 1006PhL
[GenBank EPB86304]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-87704
-86807
-86782
-88536
-8852
-91779
-642
-701
-71
-725
-645
-957
Rhizopus oryzae [Genebank AER14043]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-118487 -887
-683
-741
-799
-85
-942
-100976
-111223
-119393
-119301
-124532
The best template structure
Tang et al [28] report that Valine plays a key role in stabilizing the accurate orientation of and maintaining the enantioselectivity of the lipase [28] In comparison with our study Mucor circinelloides f circinelloides 1006PhL [EPB86304] modeled lipase showed a substitution of isoleucine (I) to valine (V) in the active site (Figure 2) However Rhizopus oryzae [AER14043] do not have this change and the modeled lipase showed slightly more favorable energy (more negative) for some substrates
Undoubtedly the new findings on the lipasesrsquo structure-function relationships are opening significant exploration ways for applications in several industries For example in industrial bioremediation our findings on functional modification of enzymes will conduct to the rational design of proteins to perhaps improve their substrate specificity enantioselectivity catalytic efficiency and thermostability Lately Zhang et al [29] were shown to improve the performance of Rhizomucor miehei lipase (RML) exhibited on yeast
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
surface in the production of human milk fat substitute (HMFS) [29] They developed an amino acid mutation in the lipase substrate-binding pocket based on protein hydrophobicity improving its activity
They used molecular coupling to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were subs Zhang M XW Yu Y Xu et al Crystal structure of lipase from Rhizopus microsporus var chinensis 2013 (en linea) [httpftpwwpdborgpubpdbvalidation_reportsl34l3w4l3w_full_validationpdf] Acceso 10122017 trates They used molecular docking to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were substrates However although we did not change any residue we obtained higher scores for oleic acid (~ 25 times for our modeled structures) and for tripalmitin ~ 95 for both modeled structures suggesting tremendous future application in bioremediation for the informed lipases here
ConclusionThe molecular docking analysis of 3D models of lipases from
Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases The structural modeling study for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase is reported in this study being Rhizopus oryzae [AER14043] the best model This study highlights fungal lipases and exemplifies its binding to the substrate ie palmitic oleic acid tripalmitin even values more favorable than the template structure However these compounds are potential substrates for these lipases and we suggest that could be evaluated in vitro This is the first study of molecular docking between fatty acids and a tripalmitin of palm oil showing an adequate binding energy accordingly to previous studies with other fungi lipases Future molecular studies will be made for redesigned the models with specifics mutations for perhaps a better interaction with pollutant fatty acids and triglycerides for applications in industry
References1 Mateos JC Rodriacuteguez JA Roussos J Cordova A Abousalham F et al
(2006) Lipase from the thermotolerant fungus Rhizopus homothallicus is more thermostable when produced using solid state fermentation than liquid fermentation procedures Enzyme Microb Technol 39(5)1042ndash1050
2 Cruz-Ramiacuterez MG Rivera-Riacuteos JM Teacutellez-Jurado A Maqueda Gaacutelvez AP Mercado-Flores Y et al (2014) Screening for thermotolerant ligninolytic fungi with laccase lipase and protease activity isolated in Mexico J Environ Biol 35(3) 521-529
3 Okogbenin OB Anisiobi GE Okogbenin EA Ojieabu A (2014) Microbiological assessment and physiochemical parameters of palm oil mill effluent collected in a local mill in Ovia North East area of Edo State Nigeria Herald journal of Microbiology Biotechnology 1(1) 1ndash9
4 Lima ACP Cammarota MC Gutarra MLE (2018) Obtaining filamentous fungi and lipases from sewage treatment plant residue for fat degradation in anaerobic reactors Peer J 6 e5368
5 Efimova E Marjakangas JM Lakaniemi AM Koskinen PE Puhakka JA (2013) Lipid profile characterization of wastewaters from different origins Water Sci Technol 68(11) 2505-2514
6 Mendoza LI (2010) Aislamiento y seleccioacuten de hongos lipoliacuteticos a partir de aceites vegetales de desecho (proveniente de frituras) utilizados en la elaboracioacuten de biodiesel [Thesis] Facultad de Ciencias bioloacutegicas Universidad Nacional Mayor de San Marcos Peru
7 Pruksatrakul T Phoopraintra P Wilairat P Chaiyen P Chantiwas R (2017) Development of a sequential injection-liquid microextraction procedure with GC-FID for analysis of short-chain fatty acids in palm oil mill effluent Talanta 165 612-618
8 Gopinath SC Anbu P Lakshmipriya T Hilda A (2013) Strategies to characterize fungal lipases for applications in medicine and dairy industry Biomed Res Int 2013 154549
9 Singh RK Feller A Roovers M Van Elder D Wauters L et al (2018) Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism RNA 24(8)1080-1092
10 Vasel B Hecht HJ Schmid RD Schomburg D (1993) 3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol J Biotechnol 28(1) 99-115
11 Meng XY Zhang HK Mezei M Cui M (2011) Molecular docking a powerful approach for structure-based drug discovery Curr Comput Aided Drug Des 7(2) 146-157
12 Ericsson DJ Kasrayan A Johansson P Bergfors T Sandstroumlm AG et al (2008) X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation J Mol Biol 376(1) 109-119
13 Nwuche CO Ogbonna JC (2011) Isolation of lipase producing fungi from palm oil mil eflfuent (POME) dumps sites al Nsukka Braz Arch Boil Technol 54(1) 113-116
14 Sigrist CJ Cerutti L de Castro E Langendijk-Genevaux PS Bulliard V et al (2010) PROSITE a protein domain database for functional characterization and annotation Nucleic Acids Res 38 D161ndashD166
15 Singh PK Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions Indian J Microbiol 52(3) 373-380
16 Morris AL MacArthur MW Hutchinson EG Thornton JM (1992) Stereochemical quality of protein structure coordinates Proteins 12(4) 345-364
17 Grosdidier A Zoete V Michielin O (2011) Swiss Dock a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res 39 W270-W277
18 Rehm S Trodler P Pleiss J (2010) Solvent-induced lid opening in lipases a molecular dynamics study Protein Sci 19(11) 2122-2130
19 Borrelli GM Trono D (2015) Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications Int J Mol Sci 16(9) 20774-20840
20 Blow D (1990) Enzymology More of the catalytic triad Nature 343 694-695
21 Juhl PB Trodler P Tyagi S Pleiss J (2009) Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking BMC Struct Biol 9 39
22 Biasini M Bienert S Waterhouse A Arnold K Studer G et al (2014) SWISS-MODEL modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res 42 W252-W258
23 Grosdidier A Zoete V Michielin O (2011) Fast docking using the CHARMM force field with EADock DSS J Comput Chem 32(10) 2149-2159
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
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DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
Abstract
Keywords
Introduction
Materials and Methods
Fungi sequence selection and alignment
Homology modeling
Molecular docking
Results and Discussion
Conclusion
References
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Table 1
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
enzymes have been used for degradation of palm oil effluent [16-8]
In silico methods helps in the predictions of enzymatic affinity activity specificity and selectivity of newly discovered proteins from structure information [9] For example molecular docking methods have also been applied successfully to predict most likely enzyme substrates with unknown experimental molecular interaction to its substrate [10] This kind of bioinformatics approaches allow the previous screening of potential target for application in bioremediation and take advantage of fungi enzymes for industrial applications
This method of predicting the enzyme-substrate complex structure can be accomplished through two unified steps first by sampling conformations of the ligand (eg fatty acids tripalmitin etc) in the active site of the protein and second by classifying these conformations by a score that ranks most negative value among all the conformations generated which indicates greater stability [11] Molecular docking studies could help to identify pollutants fatty acids suitable to be degraded by these enzymes [12]
Although it has been reported amino acid sequences of lipases from bacteria and fungi with these properties tested in vitro [13] their crystal structure in Protein Data Bank has not yet been reported Hence our study is focused on predicting the 3D structure by homology modeling from lipase amino acids sequences of Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] and subsequently the interaction of modeled structures with fatty acids and tripalmitin were analyzed by molecular docking for calculating the full fitness energy (Kcalmol)
Materials and MethodsFungi sequence selection and alignment
The amino acid sequence of the reference lipase of Rhizopus microsporus var Chinensis [EF405962] and the target amino acid sequences Mucor circinelloides f circinelloides 1006PhL [EPB86304] and R oryzae [AER14043] were obtained from
Genbank (httpwwwncbinlmnihgovgenbank) We assessed whether all had registered their 3D structure UniProt (httpwwwuniprotorguniprot) and PDB (httpwwwrcsborgpdbhomehomedo) databases We inspected and adjusted manually the sequences using the software BioEdit v725 to diminish the number of gaps and insertions Then the alignment was performed with ClustalW2 and with PROSITE online tool (httpprositeexpasyorg) was determined the corresponding active site in PROSITE tool [14]
Homology modeling
The templates crystal structures were retrieved from RCSB Protein Data Bank (PDB) in base to identity (gt30) We did the homology modeling with SWISSMODEL (httpswissmodelexpasyorginteractive) which is a fully automated protein structure homology-modeling server accessible via the ExPASy web server [15] The process considered the following steps
(i) Template identification
(ii) Template selection
(iii) Model building and
(iv) Model quality estimation
The modeled structures were further verified with programs such as PROCHEK which Checks stereochemical quality of protein structures [16] and Errat (httpwwwdoe- mbiuclaeduServicesErrathtml)
Molecular dockingMolecular docking was performed SwissDock server (http
wwwswissdockchdocking) to decipher the binding affinity and mode of interaction of the selected compounds (Scheme 1) against fungi lipases (of interest) SwissDock requires the target protein and ligand in PDB and Mol2 format respectively The ligands specified in Figure 1 As described by Grosdidier et al [17] SwissDock is based on the docking software EADock DSS whose algorithm consists of the following steps
Figure 1 Chemical structures of ligands used for molecular docking (A) Linoleic acid [PubChem 4474613] (B) linolenic acid [PubChem 5280934] (C) linolenic acid [PubChem 3802189] (D) Oleic acid [PubChem 6845860] (E) Palmitic acid [PubChem 6072466] and (F) Tripalmitin [PubChem 8214701]
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
1 Binding modes are generated either in a box (local docking) or near all target cavities (blind docking)
2 Simultaneously CHARMM energies of the binding modes are estimated on a grid
3 The binding modes with most favorable energies are evaluated with FACTS and clustered
4 Most favorable clusters are visualized online and downloaded and the obtained dock scores are reported in kcalmol [17]
We analyzed docking results thru the UCSF Chimera program (RBVI US) which provides an insight into the molecule to observe it specifically at the atomic level
Results and DiscussionThe amino acids sequences of the template and the query
lipases were aligned with Clustal (Figure 2) The query sequences of Rhizopus oryzae [AER14043] and Mucor circinelloides f circinelloides 1006PhL [EPB86304 M circinelloides] consist of 294
and 360 residues respectively but the template structure was 389 residues Manual editing query sequences were modeled from all its length and after alignment the sequence identity was 6306 for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and 7959 for Rhizopus oryzae [AER14043] respect to the sequence template Rhizopus microsporus var Chinensis [EF405962] We employed the result of alignment as criteria to build 3D structures for both query sequences by homology modeling
Lipases are extensively distributed in prokaryotes and eukaryotes Most conserved region in all these proteins focuses on a serine residue [1819] with a residue of aspartic acid and a histidine in a charge relay system Blow (1990) demonstrated their interaction and participation in a charge relay system [20] Accordingly with PROSITE our models have a serine active site VIVTGHSLGG specific for lipase but Mucor circinelloides f circinelloides 1006PhL [EPB86304] lipase model differs by one amino acid respect to the template protein (a valine replaced Isoleucine) The conserved histidine and aspartic acid residues must be highlighted in Figure 2
Figure 2 Multiple alignments of amino acidic sequences of lipases from Rhizopus microsporus var Chinensis [EF405962 Rh microspoorus] and the target amino acid sequences Mucor circinelloides f circinelloides 1006PhL [EPB86304 M circinelloides] and Rhizopus oryzae [AER14043 Rh oryzae] performed with ClustalW2 Inside the box the active site amino acids specific for lipases are shown (VIVTGHSLGG)
Several studies suggest the broad and interesting use of the study with an in silico approach Habitually they are used in the modern designs of drug to comprehend the mechanisms of pharmacological interaction at the molecular level recognizing the network and the signaling pathways of genes and the substrate-enzyme interactions Due to the great development of the in silico studies it is that the computational approaches can intensely support and help to decipher these specifics interactions between lipases and triglycerides [21] The major objective of this study was to identify the binding energy of common pollutants fatty acids
and tripalmitin present in palm oil effluents Protein structure homology modeling has become a routine technique to generate 3D models for proteins when experimental structures are unavailable The improved SWISS-MODEL pipeline makes extensive use of model quality estimation to select of most suitable templates and provides estimates of the expected accuracy of the resulting models [22]
A newly developed interactive web interface allows us to suitably search for appropriate templates using sensitive Hidden Markov
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Models searches against the SWISS-MODEL Template Library analyses alternative templates and alignments perform structural superposition and comparison and compare the resulting models using mean force potential based model quality estimation tools Model quality estimation is an essential part of protein structure predictions as the accuracy of a model determines its usefulness for practical applications [22] By the structure of lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] has not been crystallized yet here the 3D structure of the lipase was predicted by homology modeling for both species favored by the high identity respect to its template
We selected the best model among three 3D models generated after the verification of all parameters (Figure 3 amp 4) Model quality declines with decreasing sequence identity A typical model has ~1ndash2Aring root mean square deviation between the matched Cα atoms at 70 sequence identity but only 2ndash4Aring agreement at 25 sequence identity However the errors are significantly higher in the loop regions where the amino acid sequences of the target and template proteins may be completely different [23] Our Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] models have 028Aring and 007Aring root mean square deviations between the matched Cα atoms with respect to template structure respectively
Figure 3 Errat plots of modeled lipases from Mucor circinelloides f circinelloides 1006PhL (upper) [EPB86304] and Rhizopus oryzae (bottom) [AER14043] The error values for model residues as predicted by ERRAT are shown The ldquoyrdquo axis presents the error value and ldquoxrdquo axis presents the amino acid sequences of lipase An error value exceeding 99 confidence level indicates poorly modeled regions
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Figure 4 (A) The Ramachandran plot of modeled protein of Mucor circinelloides f circinelloides 1006PhL [EPB86304] (left) showing 895 of the atom residing in the most favored region 96 in the allowed region 22 in the generously allowed region and 04 residues was in the disallowed region (B) The Ramachandran plot of modeled protein of Rhizopus oryzae [AER14043] (right) showing 897 of the atom residing in the most favored region 86 in allowed region 22 in generously allowed region and 04 residues was in disallowed region
The quality of the modeled structures was first analyzed with PROCHECK by Ramachandran plots We would be expected to have a good quality model over 90 in most favored regions based on an analysis of a resolution of at least 20Aring Angstroms and R-factor of ~20
The Ramachandran plot obtained from PROCHECK program with the Mucor circinelloides f circinelloides 1006PhL [EPB86304]
lipase model showed that 896 of residues were in most favored regions 96 residues were in additional allowed regions 13 in the generously allowed regions and 04 in the disallowed regions Likewise in the same way we validated the Rhizopus oryzae [AER14043] lipase model with 897 of total residues in most favored regions 86 residues in additional allowed regions 04 in the generously allowed and disallowed regions (Figure 5)
Figure 5 (A) Oleic acid molecule binds to Rhizopus oryzae modeled lipase 3D structure into the funnel form active site (-799 estimated ΔG) (B) Mucor circinelloides f circinelloides 1006PhL modelled lipase interacts with Palmitic acid (-645 estimated ΔG) (C) Tripalmitin binds to Rhizopus oryzae modeled lipase (-942 estimated ΔG)
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
We also used ERRAT (httpnihservermbiuclaedu) which analyses the statistics of non-bonded interactions between different atom types A single output plot was produced by Errat program that gave the value of the error function against position of residues [24] An error value exceeding 99 confidence level indicates poorly modeled regions (Figure 3) Errat analyses also provide an overall quality factor expressed as the percentage of the protein for which the calculated error value falls below the 95 rejection limit Good high resolution structures generally produce values around 95 or higher For lower resolutions (25ndash3Aring) the average overall quality factor is around 91 [24] The overall quality factor assigned for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase models were 883 and 934 respectively
Accordingly with docking study published here it was predicted that modeled lipases have most effective interaction with tripalmitin (binding energy of -957Kcalmol) Docking analysis of Mucor circinelloides f circinelloides 1006PhL modeled lipase with fatty acids and tripalmitin was performed and full fitness energy was recorded The results showed a good interaction more than
one-fatty acids and tripalmiting them (Table 1) We performed the docking with SwissDock with rigid selection We conducted the same procedure with Rhizopus oryzae modelled lipase with these substrates under the same parameters and software and the results were appropriate scores for binding
As a reference a Rhizopus microsporus var Chinensis [EF405962] lipase with PDB ID 4L3W was taken for comparison where accordingly with previous reports [1825-27] We recognized that the triad ArgndashAspndashPro (RDP) is preserved in the lipase responsible for the detection of the molecules tested Our data revealed the above mentioned (VIVTGHSLGG) conserved domain in the lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] as the main site for lipase activity We also observed that fatty acids and tripalmitin binds into the pocket of the funnel shape active site of both lipases and bonding between the molecules is through hydrogen bond with bond length ~250Aring as previously reported with another ligandenzyme [15] In contrast when we analyzed the result in the lipase the docking score was favorable and fatty acid and tripalmitin molecule were bind given to the protein low fullfitness energy (Table 1)
Table 1 Molecular docking scores for target lipase structures and possible substrates found in palm oil
Source of lipase Ligand Full Fitness (Kcalmol) Estimated ∆G (kJmol)
Rhizopus microspona var Chinensis [PDB 4L3W] ()
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-96678
-105211
-112517
-106898
-114375
-108237
-626
-752
-65
-62
-804
-837
Mucor circinelloides f circinelioides 1006PhL
[GenBank EPB86304]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-87704
-86807
-86782
-88536
-8852
-91779
-642
-701
-71
-725
-645
-957
Rhizopus oryzae [Genebank AER14043]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-118487 -887
-683
-741
-799
-85
-942
-100976
-111223
-119393
-119301
-124532
The best template structure
Tang et al [28] report that Valine plays a key role in stabilizing the accurate orientation of and maintaining the enantioselectivity of the lipase [28] In comparison with our study Mucor circinelloides f circinelloides 1006PhL [EPB86304] modeled lipase showed a substitution of isoleucine (I) to valine (V) in the active site (Figure 2) However Rhizopus oryzae [AER14043] do not have this change and the modeled lipase showed slightly more favorable energy (more negative) for some substrates
Undoubtedly the new findings on the lipasesrsquo structure-function relationships are opening significant exploration ways for applications in several industries For example in industrial bioremediation our findings on functional modification of enzymes will conduct to the rational design of proteins to perhaps improve their substrate specificity enantioselectivity catalytic efficiency and thermostability Lately Zhang et al [29] were shown to improve the performance of Rhizomucor miehei lipase (RML) exhibited on yeast
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
surface in the production of human milk fat substitute (HMFS) [29] They developed an amino acid mutation in the lipase substrate-binding pocket based on protein hydrophobicity improving its activity
They used molecular coupling to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were subs Zhang M XW Yu Y Xu et al Crystal structure of lipase from Rhizopus microsporus var chinensis 2013 (en linea) [httpftpwwpdborgpubpdbvalidation_reportsl34l3w4l3w_full_validationpdf] Acceso 10122017 trates They used molecular docking to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were substrates However although we did not change any residue we obtained higher scores for oleic acid (~ 25 times for our modeled structures) and for tripalmitin ~ 95 for both modeled structures suggesting tremendous future application in bioremediation for the informed lipases here
ConclusionThe molecular docking analysis of 3D models of lipases from
Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases The structural modeling study for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase is reported in this study being Rhizopus oryzae [AER14043] the best model This study highlights fungal lipases and exemplifies its binding to the substrate ie palmitic oleic acid tripalmitin even values more favorable than the template structure However these compounds are potential substrates for these lipases and we suggest that could be evaluated in vitro This is the first study of molecular docking between fatty acids and a tripalmitin of palm oil showing an adequate binding energy accordingly to previous studies with other fungi lipases Future molecular studies will be made for redesigned the models with specifics mutations for perhaps a better interaction with pollutant fatty acids and triglycerides for applications in industry
References1 Mateos JC Rodriacuteguez JA Roussos J Cordova A Abousalham F et al
(2006) Lipase from the thermotolerant fungus Rhizopus homothallicus is more thermostable when produced using solid state fermentation than liquid fermentation procedures Enzyme Microb Technol 39(5)1042ndash1050
2 Cruz-Ramiacuterez MG Rivera-Riacuteos JM Teacutellez-Jurado A Maqueda Gaacutelvez AP Mercado-Flores Y et al (2014) Screening for thermotolerant ligninolytic fungi with laccase lipase and protease activity isolated in Mexico J Environ Biol 35(3) 521-529
3 Okogbenin OB Anisiobi GE Okogbenin EA Ojieabu A (2014) Microbiological assessment and physiochemical parameters of palm oil mill effluent collected in a local mill in Ovia North East area of Edo State Nigeria Herald journal of Microbiology Biotechnology 1(1) 1ndash9
4 Lima ACP Cammarota MC Gutarra MLE (2018) Obtaining filamentous fungi and lipases from sewage treatment plant residue for fat degradation in anaerobic reactors Peer J 6 e5368
5 Efimova E Marjakangas JM Lakaniemi AM Koskinen PE Puhakka JA (2013) Lipid profile characterization of wastewaters from different origins Water Sci Technol 68(11) 2505-2514
6 Mendoza LI (2010) Aislamiento y seleccioacuten de hongos lipoliacuteticos a partir de aceites vegetales de desecho (proveniente de frituras) utilizados en la elaboracioacuten de biodiesel [Thesis] Facultad de Ciencias bioloacutegicas Universidad Nacional Mayor de San Marcos Peru
7 Pruksatrakul T Phoopraintra P Wilairat P Chaiyen P Chantiwas R (2017) Development of a sequential injection-liquid microextraction procedure with GC-FID for analysis of short-chain fatty acids in palm oil mill effluent Talanta 165 612-618
8 Gopinath SC Anbu P Lakshmipriya T Hilda A (2013) Strategies to characterize fungal lipases for applications in medicine and dairy industry Biomed Res Int 2013 154549
9 Singh RK Feller A Roovers M Van Elder D Wauters L et al (2018) Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism RNA 24(8)1080-1092
10 Vasel B Hecht HJ Schmid RD Schomburg D (1993) 3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol J Biotechnol 28(1) 99-115
11 Meng XY Zhang HK Mezei M Cui M (2011) Molecular docking a powerful approach for structure-based drug discovery Curr Comput Aided Drug Des 7(2) 146-157
12 Ericsson DJ Kasrayan A Johansson P Bergfors T Sandstroumlm AG et al (2008) X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation J Mol Biol 376(1) 109-119
13 Nwuche CO Ogbonna JC (2011) Isolation of lipase producing fungi from palm oil mil eflfuent (POME) dumps sites al Nsukka Braz Arch Boil Technol 54(1) 113-116
14 Sigrist CJ Cerutti L de Castro E Langendijk-Genevaux PS Bulliard V et al (2010) PROSITE a protein domain database for functional characterization and annotation Nucleic Acids Res 38 D161ndashD166
15 Singh PK Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions Indian J Microbiol 52(3) 373-380
16 Morris AL MacArthur MW Hutchinson EG Thornton JM (1992) Stereochemical quality of protein structure coordinates Proteins 12(4) 345-364
17 Grosdidier A Zoete V Michielin O (2011) Swiss Dock a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res 39 W270-W277
18 Rehm S Trodler P Pleiss J (2010) Solvent-induced lid opening in lipases a molecular dynamics study Protein Sci 19(11) 2122-2130
19 Borrelli GM Trono D (2015) Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications Int J Mol Sci 16(9) 20774-20840
20 Blow D (1990) Enzymology More of the catalytic triad Nature 343 694-695
21 Juhl PB Trodler P Tyagi S Pleiss J (2009) Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking BMC Struct Biol 9 39
22 Biasini M Bienert S Waterhouse A Arnold K Studer G et al (2014) SWISS-MODEL modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res 42 W252-W258
23 Grosdidier A Zoete V Michielin O (2011) Fast docking using the CHARMM force field with EADock DSS J Comput Chem 32(10) 2149-2159
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
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DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
Abstract
Keywords
Introduction
Materials and Methods
Fungi sequence selection and alignment
Homology modeling
Molecular docking
Results and Discussion
Conclusion
References
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Table 1
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
1 Binding modes are generated either in a box (local docking) or near all target cavities (blind docking)
2 Simultaneously CHARMM energies of the binding modes are estimated on a grid
3 The binding modes with most favorable energies are evaluated with FACTS and clustered
4 Most favorable clusters are visualized online and downloaded and the obtained dock scores are reported in kcalmol [17]
We analyzed docking results thru the UCSF Chimera program (RBVI US) which provides an insight into the molecule to observe it specifically at the atomic level
Results and DiscussionThe amino acids sequences of the template and the query
lipases were aligned with Clustal (Figure 2) The query sequences of Rhizopus oryzae [AER14043] and Mucor circinelloides f circinelloides 1006PhL [EPB86304 M circinelloides] consist of 294
and 360 residues respectively but the template structure was 389 residues Manual editing query sequences were modeled from all its length and after alignment the sequence identity was 6306 for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and 7959 for Rhizopus oryzae [AER14043] respect to the sequence template Rhizopus microsporus var Chinensis [EF405962] We employed the result of alignment as criteria to build 3D structures for both query sequences by homology modeling
Lipases are extensively distributed in prokaryotes and eukaryotes Most conserved region in all these proteins focuses on a serine residue [1819] with a residue of aspartic acid and a histidine in a charge relay system Blow (1990) demonstrated their interaction and participation in a charge relay system [20] Accordingly with PROSITE our models have a serine active site VIVTGHSLGG specific for lipase but Mucor circinelloides f circinelloides 1006PhL [EPB86304] lipase model differs by one amino acid respect to the template protein (a valine replaced Isoleucine) The conserved histidine and aspartic acid residues must be highlighted in Figure 2
Figure 2 Multiple alignments of amino acidic sequences of lipases from Rhizopus microsporus var Chinensis [EF405962 Rh microspoorus] and the target amino acid sequences Mucor circinelloides f circinelloides 1006PhL [EPB86304 M circinelloides] and Rhizopus oryzae [AER14043 Rh oryzae] performed with ClustalW2 Inside the box the active site amino acids specific for lipases are shown (VIVTGHSLGG)
Several studies suggest the broad and interesting use of the study with an in silico approach Habitually they are used in the modern designs of drug to comprehend the mechanisms of pharmacological interaction at the molecular level recognizing the network and the signaling pathways of genes and the substrate-enzyme interactions Due to the great development of the in silico studies it is that the computational approaches can intensely support and help to decipher these specifics interactions between lipases and triglycerides [21] The major objective of this study was to identify the binding energy of common pollutants fatty acids
and tripalmitin present in palm oil effluents Protein structure homology modeling has become a routine technique to generate 3D models for proteins when experimental structures are unavailable The improved SWISS-MODEL pipeline makes extensive use of model quality estimation to select of most suitable templates and provides estimates of the expected accuracy of the resulting models [22]
A newly developed interactive web interface allows us to suitably search for appropriate templates using sensitive Hidden Markov
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Models searches against the SWISS-MODEL Template Library analyses alternative templates and alignments perform structural superposition and comparison and compare the resulting models using mean force potential based model quality estimation tools Model quality estimation is an essential part of protein structure predictions as the accuracy of a model determines its usefulness for practical applications [22] By the structure of lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] has not been crystallized yet here the 3D structure of the lipase was predicted by homology modeling for both species favored by the high identity respect to its template
We selected the best model among three 3D models generated after the verification of all parameters (Figure 3 amp 4) Model quality declines with decreasing sequence identity A typical model has ~1ndash2Aring root mean square deviation between the matched Cα atoms at 70 sequence identity but only 2ndash4Aring agreement at 25 sequence identity However the errors are significantly higher in the loop regions where the amino acid sequences of the target and template proteins may be completely different [23] Our Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] models have 028Aring and 007Aring root mean square deviations between the matched Cα atoms with respect to template structure respectively
Figure 3 Errat plots of modeled lipases from Mucor circinelloides f circinelloides 1006PhL (upper) [EPB86304] and Rhizopus oryzae (bottom) [AER14043] The error values for model residues as predicted by ERRAT are shown The ldquoyrdquo axis presents the error value and ldquoxrdquo axis presents the amino acid sequences of lipase An error value exceeding 99 confidence level indicates poorly modeled regions
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Figure 4 (A) The Ramachandran plot of modeled protein of Mucor circinelloides f circinelloides 1006PhL [EPB86304] (left) showing 895 of the atom residing in the most favored region 96 in the allowed region 22 in the generously allowed region and 04 residues was in the disallowed region (B) The Ramachandran plot of modeled protein of Rhizopus oryzae [AER14043] (right) showing 897 of the atom residing in the most favored region 86 in allowed region 22 in generously allowed region and 04 residues was in disallowed region
The quality of the modeled structures was first analyzed with PROCHECK by Ramachandran plots We would be expected to have a good quality model over 90 in most favored regions based on an analysis of a resolution of at least 20Aring Angstroms and R-factor of ~20
The Ramachandran plot obtained from PROCHECK program with the Mucor circinelloides f circinelloides 1006PhL [EPB86304]
lipase model showed that 896 of residues were in most favored regions 96 residues were in additional allowed regions 13 in the generously allowed regions and 04 in the disallowed regions Likewise in the same way we validated the Rhizopus oryzae [AER14043] lipase model with 897 of total residues in most favored regions 86 residues in additional allowed regions 04 in the generously allowed and disallowed regions (Figure 5)
Figure 5 (A) Oleic acid molecule binds to Rhizopus oryzae modeled lipase 3D structure into the funnel form active site (-799 estimated ΔG) (B) Mucor circinelloides f circinelloides 1006PhL modelled lipase interacts with Palmitic acid (-645 estimated ΔG) (C) Tripalmitin binds to Rhizopus oryzae modeled lipase (-942 estimated ΔG)
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
We also used ERRAT (httpnihservermbiuclaedu) which analyses the statistics of non-bonded interactions between different atom types A single output plot was produced by Errat program that gave the value of the error function against position of residues [24] An error value exceeding 99 confidence level indicates poorly modeled regions (Figure 3) Errat analyses also provide an overall quality factor expressed as the percentage of the protein for which the calculated error value falls below the 95 rejection limit Good high resolution structures generally produce values around 95 or higher For lower resolutions (25ndash3Aring) the average overall quality factor is around 91 [24] The overall quality factor assigned for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase models were 883 and 934 respectively
Accordingly with docking study published here it was predicted that modeled lipases have most effective interaction with tripalmitin (binding energy of -957Kcalmol) Docking analysis of Mucor circinelloides f circinelloides 1006PhL modeled lipase with fatty acids and tripalmitin was performed and full fitness energy was recorded The results showed a good interaction more than
one-fatty acids and tripalmiting them (Table 1) We performed the docking with SwissDock with rigid selection We conducted the same procedure with Rhizopus oryzae modelled lipase with these substrates under the same parameters and software and the results were appropriate scores for binding
As a reference a Rhizopus microsporus var Chinensis [EF405962] lipase with PDB ID 4L3W was taken for comparison where accordingly with previous reports [1825-27] We recognized that the triad ArgndashAspndashPro (RDP) is preserved in the lipase responsible for the detection of the molecules tested Our data revealed the above mentioned (VIVTGHSLGG) conserved domain in the lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] as the main site for lipase activity We also observed that fatty acids and tripalmitin binds into the pocket of the funnel shape active site of both lipases and bonding between the molecules is through hydrogen bond with bond length ~250Aring as previously reported with another ligandenzyme [15] In contrast when we analyzed the result in the lipase the docking score was favorable and fatty acid and tripalmitin molecule were bind given to the protein low fullfitness energy (Table 1)
Table 1 Molecular docking scores for target lipase structures and possible substrates found in palm oil
Source of lipase Ligand Full Fitness (Kcalmol) Estimated ∆G (kJmol)
Rhizopus microspona var Chinensis [PDB 4L3W] ()
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-96678
-105211
-112517
-106898
-114375
-108237
-626
-752
-65
-62
-804
-837
Mucor circinelloides f circinelioides 1006PhL
[GenBank EPB86304]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-87704
-86807
-86782
-88536
-8852
-91779
-642
-701
-71
-725
-645
-957
Rhizopus oryzae [Genebank AER14043]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-118487 -887
-683
-741
-799
-85
-942
-100976
-111223
-119393
-119301
-124532
The best template structure
Tang et al [28] report that Valine plays a key role in stabilizing the accurate orientation of and maintaining the enantioselectivity of the lipase [28] In comparison with our study Mucor circinelloides f circinelloides 1006PhL [EPB86304] modeled lipase showed a substitution of isoleucine (I) to valine (V) in the active site (Figure 2) However Rhizopus oryzae [AER14043] do not have this change and the modeled lipase showed slightly more favorable energy (more negative) for some substrates
Undoubtedly the new findings on the lipasesrsquo structure-function relationships are opening significant exploration ways for applications in several industries For example in industrial bioremediation our findings on functional modification of enzymes will conduct to the rational design of proteins to perhaps improve their substrate specificity enantioselectivity catalytic efficiency and thermostability Lately Zhang et al [29] were shown to improve the performance of Rhizomucor miehei lipase (RML) exhibited on yeast
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
surface in the production of human milk fat substitute (HMFS) [29] They developed an amino acid mutation in the lipase substrate-binding pocket based on protein hydrophobicity improving its activity
They used molecular coupling to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were subs Zhang M XW Yu Y Xu et al Crystal structure of lipase from Rhizopus microsporus var chinensis 2013 (en linea) [httpftpwwpdborgpubpdbvalidation_reportsl34l3w4l3w_full_validationpdf] Acceso 10122017 trates They used molecular docking to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were substrates However although we did not change any residue we obtained higher scores for oleic acid (~ 25 times for our modeled structures) and for tripalmitin ~ 95 for both modeled structures suggesting tremendous future application in bioremediation for the informed lipases here
ConclusionThe molecular docking analysis of 3D models of lipases from
Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases The structural modeling study for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase is reported in this study being Rhizopus oryzae [AER14043] the best model This study highlights fungal lipases and exemplifies its binding to the substrate ie palmitic oleic acid tripalmitin even values more favorable than the template structure However these compounds are potential substrates for these lipases and we suggest that could be evaluated in vitro This is the first study of molecular docking between fatty acids and a tripalmitin of palm oil showing an adequate binding energy accordingly to previous studies with other fungi lipases Future molecular studies will be made for redesigned the models with specifics mutations for perhaps a better interaction with pollutant fatty acids and triglycerides for applications in industry
References1 Mateos JC Rodriacuteguez JA Roussos J Cordova A Abousalham F et al
(2006) Lipase from the thermotolerant fungus Rhizopus homothallicus is more thermostable when produced using solid state fermentation than liquid fermentation procedures Enzyme Microb Technol 39(5)1042ndash1050
2 Cruz-Ramiacuterez MG Rivera-Riacuteos JM Teacutellez-Jurado A Maqueda Gaacutelvez AP Mercado-Flores Y et al (2014) Screening for thermotolerant ligninolytic fungi with laccase lipase and protease activity isolated in Mexico J Environ Biol 35(3) 521-529
3 Okogbenin OB Anisiobi GE Okogbenin EA Ojieabu A (2014) Microbiological assessment and physiochemical parameters of palm oil mill effluent collected in a local mill in Ovia North East area of Edo State Nigeria Herald journal of Microbiology Biotechnology 1(1) 1ndash9
4 Lima ACP Cammarota MC Gutarra MLE (2018) Obtaining filamentous fungi and lipases from sewage treatment plant residue for fat degradation in anaerobic reactors Peer J 6 e5368
5 Efimova E Marjakangas JM Lakaniemi AM Koskinen PE Puhakka JA (2013) Lipid profile characterization of wastewaters from different origins Water Sci Technol 68(11) 2505-2514
6 Mendoza LI (2010) Aislamiento y seleccioacuten de hongos lipoliacuteticos a partir de aceites vegetales de desecho (proveniente de frituras) utilizados en la elaboracioacuten de biodiesel [Thesis] Facultad de Ciencias bioloacutegicas Universidad Nacional Mayor de San Marcos Peru
7 Pruksatrakul T Phoopraintra P Wilairat P Chaiyen P Chantiwas R (2017) Development of a sequential injection-liquid microextraction procedure with GC-FID for analysis of short-chain fatty acids in palm oil mill effluent Talanta 165 612-618
8 Gopinath SC Anbu P Lakshmipriya T Hilda A (2013) Strategies to characterize fungal lipases for applications in medicine and dairy industry Biomed Res Int 2013 154549
9 Singh RK Feller A Roovers M Van Elder D Wauters L et al (2018) Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism RNA 24(8)1080-1092
10 Vasel B Hecht HJ Schmid RD Schomburg D (1993) 3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol J Biotechnol 28(1) 99-115
11 Meng XY Zhang HK Mezei M Cui M (2011) Molecular docking a powerful approach for structure-based drug discovery Curr Comput Aided Drug Des 7(2) 146-157
12 Ericsson DJ Kasrayan A Johansson P Bergfors T Sandstroumlm AG et al (2008) X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation J Mol Biol 376(1) 109-119
13 Nwuche CO Ogbonna JC (2011) Isolation of lipase producing fungi from palm oil mil eflfuent (POME) dumps sites al Nsukka Braz Arch Boil Technol 54(1) 113-116
14 Sigrist CJ Cerutti L de Castro E Langendijk-Genevaux PS Bulliard V et al (2010) PROSITE a protein domain database for functional characterization and annotation Nucleic Acids Res 38 D161ndashD166
15 Singh PK Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions Indian J Microbiol 52(3) 373-380
16 Morris AL MacArthur MW Hutchinson EG Thornton JM (1992) Stereochemical quality of protein structure coordinates Proteins 12(4) 345-364
17 Grosdidier A Zoete V Michielin O (2011) Swiss Dock a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res 39 W270-W277
18 Rehm S Trodler P Pleiss J (2010) Solvent-induced lid opening in lipases a molecular dynamics study Protein Sci 19(11) 2122-2130
19 Borrelli GM Trono D (2015) Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications Int J Mol Sci 16(9) 20774-20840
20 Blow D (1990) Enzymology More of the catalytic triad Nature 343 694-695
21 Juhl PB Trodler P Tyagi S Pleiss J (2009) Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking BMC Struct Biol 9 39
22 Biasini M Bienert S Waterhouse A Arnold K Studer G et al (2014) SWISS-MODEL modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res 42 W252-W258
23 Grosdidier A Zoete V Michielin O (2011) Fast docking using the CHARMM force field with EADock DSS J Comput Chem 32(10) 2149-2159
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
Archives of Organic and Inorganic Chemical Sciences
Assets of Publishing with us
bull Global archiving of articles
bull Immediate unrestricted online access
bull Rigorous Peer Review Process
bull Authors Retain Copyrights
bull Unique DOI for all articles
This work is licensed under CreativeCommons Attribution 40 License
To Submit Your Article Click Here Submit Article
DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
Abstract
Keywords
Introduction
Materials and Methods
Fungi sequence selection and alignment
Homology modeling
Molecular docking
Results and Discussion
Conclusion
References
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Table 1
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Models searches against the SWISS-MODEL Template Library analyses alternative templates and alignments perform structural superposition and comparison and compare the resulting models using mean force potential based model quality estimation tools Model quality estimation is an essential part of protein structure predictions as the accuracy of a model determines its usefulness for practical applications [22] By the structure of lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] has not been crystallized yet here the 3D structure of the lipase was predicted by homology modeling for both species favored by the high identity respect to its template
We selected the best model among three 3D models generated after the verification of all parameters (Figure 3 amp 4) Model quality declines with decreasing sequence identity A typical model has ~1ndash2Aring root mean square deviation between the matched Cα atoms at 70 sequence identity but only 2ndash4Aring agreement at 25 sequence identity However the errors are significantly higher in the loop regions where the amino acid sequences of the target and template proteins may be completely different [23] Our Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] models have 028Aring and 007Aring root mean square deviations between the matched Cα atoms with respect to template structure respectively
Figure 3 Errat plots of modeled lipases from Mucor circinelloides f circinelloides 1006PhL (upper) [EPB86304] and Rhizopus oryzae (bottom) [AER14043] The error values for model residues as predicted by ERRAT are shown The ldquoyrdquo axis presents the error value and ldquoxrdquo axis presents the amino acid sequences of lipase An error value exceeding 99 confidence level indicates poorly modeled regions
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Figure 4 (A) The Ramachandran plot of modeled protein of Mucor circinelloides f circinelloides 1006PhL [EPB86304] (left) showing 895 of the atom residing in the most favored region 96 in the allowed region 22 in the generously allowed region and 04 residues was in the disallowed region (B) The Ramachandran plot of modeled protein of Rhizopus oryzae [AER14043] (right) showing 897 of the atom residing in the most favored region 86 in allowed region 22 in generously allowed region and 04 residues was in disallowed region
The quality of the modeled structures was first analyzed with PROCHECK by Ramachandran plots We would be expected to have a good quality model over 90 in most favored regions based on an analysis of a resolution of at least 20Aring Angstroms and R-factor of ~20
The Ramachandran plot obtained from PROCHECK program with the Mucor circinelloides f circinelloides 1006PhL [EPB86304]
lipase model showed that 896 of residues were in most favored regions 96 residues were in additional allowed regions 13 in the generously allowed regions and 04 in the disallowed regions Likewise in the same way we validated the Rhizopus oryzae [AER14043] lipase model with 897 of total residues in most favored regions 86 residues in additional allowed regions 04 in the generously allowed and disallowed regions (Figure 5)
Figure 5 (A) Oleic acid molecule binds to Rhizopus oryzae modeled lipase 3D structure into the funnel form active site (-799 estimated ΔG) (B) Mucor circinelloides f circinelloides 1006PhL modelled lipase interacts with Palmitic acid (-645 estimated ΔG) (C) Tripalmitin binds to Rhizopus oryzae modeled lipase (-942 estimated ΔG)
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
We also used ERRAT (httpnihservermbiuclaedu) which analyses the statistics of non-bonded interactions between different atom types A single output plot was produced by Errat program that gave the value of the error function against position of residues [24] An error value exceeding 99 confidence level indicates poorly modeled regions (Figure 3) Errat analyses also provide an overall quality factor expressed as the percentage of the protein for which the calculated error value falls below the 95 rejection limit Good high resolution structures generally produce values around 95 or higher For lower resolutions (25ndash3Aring) the average overall quality factor is around 91 [24] The overall quality factor assigned for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase models were 883 and 934 respectively
Accordingly with docking study published here it was predicted that modeled lipases have most effective interaction with tripalmitin (binding energy of -957Kcalmol) Docking analysis of Mucor circinelloides f circinelloides 1006PhL modeled lipase with fatty acids and tripalmitin was performed and full fitness energy was recorded The results showed a good interaction more than
one-fatty acids and tripalmiting them (Table 1) We performed the docking with SwissDock with rigid selection We conducted the same procedure with Rhizopus oryzae modelled lipase with these substrates under the same parameters and software and the results were appropriate scores for binding
As a reference a Rhizopus microsporus var Chinensis [EF405962] lipase with PDB ID 4L3W was taken for comparison where accordingly with previous reports [1825-27] We recognized that the triad ArgndashAspndashPro (RDP) is preserved in the lipase responsible for the detection of the molecules tested Our data revealed the above mentioned (VIVTGHSLGG) conserved domain in the lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] as the main site for lipase activity We also observed that fatty acids and tripalmitin binds into the pocket of the funnel shape active site of both lipases and bonding between the molecules is through hydrogen bond with bond length ~250Aring as previously reported with another ligandenzyme [15] In contrast when we analyzed the result in the lipase the docking score was favorable and fatty acid and tripalmitin molecule were bind given to the protein low fullfitness energy (Table 1)
Table 1 Molecular docking scores for target lipase structures and possible substrates found in palm oil
Source of lipase Ligand Full Fitness (Kcalmol) Estimated ∆G (kJmol)
Rhizopus microspona var Chinensis [PDB 4L3W] ()
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-96678
-105211
-112517
-106898
-114375
-108237
-626
-752
-65
-62
-804
-837
Mucor circinelloides f circinelioides 1006PhL
[GenBank EPB86304]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-87704
-86807
-86782
-88536
-8852
-91779
-642
-701
-71
-725
-645
-957
Rhizopus oryzae [Genebank AER14043]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-118487 -887
-683
-741
-799
-85
-942
-100976
-111223
-119393
-119301
-124532
The best template structure
Tang et al [28] report that Valine plays a key role in stabilizing the accurate orientation of and maintaining the enantioselectivity of the lipase [28] In comparison with our study Mucor circinelloides f circinelloides 1006PhL [EPB86304] modeled lipase showed a substitution of isoleucine (I) to valine (V) in the active site (Figure 2) However Rhizopus oryzae [AER14043] do not have this change and the modeled lipase showed slightly more favorable energy (more negative) for some substrates
Undoubtedly the new findings on the lipasesrsquo structure-function relationships are opening significant exploration ways for applications in several industries For example in industrial bioremediation our findings on functional modification of enzymes will conduct to the rational design of proteins to perhaps improve their substrate specificity enantioselectivity catalytic efficiency and thermostability Lately Zhang et al [29] were shown to improve the performance of Rhizomucor miehei lipase (RML) exhibited on yeast
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
surface in the production of human milk fat substitute (HMFS) [29] They developed an amino acid mutation in the lipase substrate-binding pocket based on protein hydrophobicity improving its activity
They used molecular coupling to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were subs Zhang M XW Yu Y Xu et al Crystal structure of lipase from Rhizopus microsporus var chinensis 2013 (en linea) [httpftpwwpdborgpubpdbvalidation_reportsl34l3w4l3w_full_validationpdf] Acceso 10122017 trates They used molecular docking to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were substrates However although we did not change any residue we obtained higher scores for oleic acid (~ 25 times for our modeled structures) and for tripalmitin ~ 95 for both modeled structures suggesting tremendous future application in bioremediation for the informed lipases here
ConclusionThe molecular docking analysis of 3D models of lipases from
Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases The structural modeling study for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase is reported in this study being Rhizopus oryzae [AER14043] the best model This study highlights fungal lipases and exemplifies its binding to the substrate ie palmitic oleic acid tripalmitin even values more favorable than the template structure However these compounds are potential substrates for these lipases and we suggest that could be evaluated in vitro This is the first study of molecular docking between fatty acids and a tripalmitin of palm oil showing an adequate binding energy accordingly to previous studies with other fungi lipases Future molecular studies will be made for redesigned the models with specifics mutations for perhaps a better interaction with pollutant fatty acids and triglycerides for applications in industry
References1 Mateos JC Rodriacuteguez JA Roussos J Cordova A Abousalham F et al
(2006) Lipase from the thermotolerant fungus Rhizopus homothallicus is more thermostable when produced using solid state fermentation than liquid fermentation procedures Enzyme Microb Technol 39(5)1042ndash1050
2 Cruz-Ramiacuterez MG Rivera-Riacuteos JM Teacutellez-Jurado A Maqueda Gaacutelvez AP Mercado-Flores Y et al (2014) Screening for thermotolerant ligninolytic fungi with laccase lipase and protease activity isolated in Mexico J Environ Biol 35(3) 521-529
3 Okogbenin OB Anisiobi GE Okogbenin EA Ojieabu A (2014) Microbiological assessment and physiochemical parameters of palm oil mill effluent collected in a local mill in Ovia North East area of Edo State Nigeria Herald journal of Microbiology Biotechnology 1(1) 1ndash9
4 Lima ACP Cammarota MC Gutarra MLE (2018) Obtaining filamentous fungi and lipases from sewage treatment plant residue for fat degradation in anaerobic reactors Peer J 6 e5368
5 Efimova E Marjakangas JM Lakaniemi AM Koskinen PE Puhakka JA (2013) Lipid profile characterization of wastewaters from different origins Water Sci Technol 68(11) 2505-2514
6 Mendoza LI (2010) Aislamiento y seleccioacuten de hongos lipoliacuteticos a partir de aceites vegetales de desecho (proveniente de frituras) utilizados en la elaboracioacuten de biodiesel [Thesis] Facultad de Ciencias bioloacutegicas Universidad Nacional Mayor de San Marcos Peru
7 Pruksatrakul T Phoopraintra P Wilairat P Chaiyen P Chantiwas R (2017) Development of a sequential injection-liquid microextraction procedure with GC-FID for analysis of short-chain fatty acids in palm oil mill effluent Talanta 165 612-618
8 Gopinath SC Anbu P Lakshmipriya T Hilda A (2013) Strategies to characterize fungal lipases for applications in medicine and dairy industry Biomed Res Int 2013 154549
9 Singh RK Feller A Roovers M Van Elder D Wauters L et al (2018) Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism RNA 24(8)1080-1092
10 Vasel B Hecht HJ Schmid RD Schomburg D (1993) 3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol J Biotechnol 28(1) 99-115
11 Meng XY Zhang HK Mezei M Cui M (2011) Molecular docking a powerful approach for structure-based drug discovery Curr Comput Aided Drug Des 7(2) 146-157
12 Ericsson DJ Kasrayan A Johansson P Bergfors T Sandstroumlm AG et al (2008) X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation J Mol Biol 376(1) 109-119
13 Nwuche CO Ogbonna JC (2011) Isolation of lipase producing fungi from palm oil mil eflfuent (POME) dumps sites al Nsukka Braz Arch Boil Technol 54(1) 113-116
14 Sigrist CJ Cerutti L de Castro E Langendijk-Genevaux PS Bulliard V et al (2010) PROSITE a protein domain database for functional characterization and annotation Nucleic Acids Res 38 D161ndashD166
15 Singh PK Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions Indian J Microbiol 52(3) 373-380
16 Morris AL MacArthur MW Hutchinson EG Thornton JM (1992) Stereochemical quality of protein structure coordinates Proteins 12(4) 345-364
17 Grosdidier A Zoete V Michielin O (2011) Swiss Dock a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res 39 W270-W277
18 Rehm S Trodler P Pleiss J (2010) Solvent-induced lid opening in lipases a molecular dynamics study Protein Sci 19(11) 2122-2130
19 Borrelli GM Trono D (2015) Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications Int J Mol Sci 16(9) 20774-20840
20 Blow D (1990) Enzymology More of the catalytic triad Nature 343 694-695
21 Juhl PB Trodler P Tyagi S Pleiss J (2009) Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking BMC Struct Biol 9 39
22 Biasini M Bienert S Waterhouse A Arnold K Studer G et al (2014) SWISS-MODEL modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res 42 W252-W258
23 Grosdidier A Zoete V Michielin O (2011) Fast docking using the CHARMM force field with EADock DSS J Comput Chem 32(10) 2149-2159
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
Archives of Organic and Inorganic Chemical Sciences
Assets of Publishing with us
bull Global archiving of articles
bull Immediate unrestricted online access
bull Rigorous Peer Review Process
bull Authors Retain Copyrights
bull Unique DOI for all articles
This work is licensed under CreativeCommons Attribution 40 License
To Submit Your Article Click Here Submit Article
DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
Abstract
Keywords
Introduction
Materials and Methods
Fungi sequence selection and alignment
Homology modeling
Molecular docking
Results and Discussion
Conclusion
References
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Table 1
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
Figure 4 (A) The Ramachandran plot of modeled protein of Mucor circinelloides f circinelloides 1006PhL [EPB86304] (left) showing 895 of the atom residing in the most favored region 96 in the allowed region 22 in the generously allowed region and 04 residues was in the disallowed region (B) The Ramachandran plot of modeled protein of Rhizopus oryzae [AER14043] (right) showing 897 of the atom residing in the most favored region 86 in allowed region 22 in generously allowed region and 04 residues was in disallowed region
The quality of the modeled structures was first analyzed with PROCHECK by Ramachandran plots We would be expected to have a good quality model over 90 in most favored regions based on an analysis of a resolution of at least 20Aring Angstroms and R-factor of ~20
The Ramachandran plot obtained from PROCHECK program with the Mucor circinelloides f circinelloides 1006PhL [EPB86304]
lipase model showed that 896 of residues were in most favored regions 96 residues were in additional allowed regions 13 in the generously allowed regions and 04 in the disallowed regions Likewise in the same way we validated the Rhizopus oryzae [AER14043] lipase model with 897 of total residues in most favored regions 86 residues in additional allowed regions 04 in the generously allowed and disallowed regions (Figure 5)
Figure 5 (A) Oleic acid molecule binds to Rhizopus oryzae modeled lipase 3D structure into the funnel form active site (-799 estimated ΔG) (B) Mucor circinelloides f circinelloides 1006PhL modelled lipase interacts with Palmitic acid (-645 estimated ΔG) (C) Tripalmitin binds to Rhizopus oryzae modeled lipase (-942 estimated ΔG)
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
We also used ERRAT (httpnihservermbiuclaedu) which analyses the statistics of non-bonded interactions between different atom types A single output plot was produced by Errat program that gave the value of the error function against position of residues [24] An error value exceeding 99 confidence level indicates poorly modeled regions (Figure 3) Errat analyses also provide an overall quality factor expressed as the percentage of the protein for which the calculated error value falls below the 95 rejection limit Good high resolution structures generally produce values around 95 or higher For lower resolutions (25ndash3Aring) the average overall quality factor is around 91 [24] The overall quality factor assigned for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase models were 883 and 934 respectively
Accordingly with docking study published here it was predicted that modeled lipases have most effective interaction with tripalmitin (binding energy of -957Kcalmol) Docking analysis of Mucor circinelloides f circinelloides 1006PhL modeled lipase with fatty acids and tripalmitin was performed and full fitness energy was recorded The results showed a good interaction more than
one-fatty acids and tripalmiting them (Table 1) We performed the docking with SwissDock with rigid selection We conducted the same procedure with Rhizopus oryzae modelled lipase with these substrates under the same parameters and software and the results were appropriate scores for binding
As a reference a Rhizopus microsporus var Chinensis [EF405962] lipase with PDB ID 4L3W was taken for comparison where accordingly with previous reports [1825-27] We recognized that the triad ArgndashAspndashPro (RDP) is preserved in the lipase responsible for the detection of the molecules tested Our data revealed the above mentioned (VIVTGHSLGG) conserved domain in the lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] as the main site for lipase activity We also observed that fatty acids and tripalmitin binds into the pocket of the funnel shape active site of both lipases and bonding between the molecules is through hydrogen bond with bond length ~250Aring as previously reported with another ligandenzyme [15] In contrast when we analyzed the result in the lipase the docking score was favorable and fatty acid and tripalmitin molecule were bind given to the protein low fullfitness energy (Table 1)
Table 1 Molecular docking scores for target lipase structures and possible substrates found in palm oil
Source of lipase Ligand Full Fitness (Kcalmol) Estimated ∆G (kJmol)
Rhizopus microspona var Chinensis [PDB 4L3W] ()
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-96678
-105211
-112517
-106898
-114375
-108237
-626
-752
-65
-62
-804
-837
Mucor circinelloides f circinelioides 1006PhL
[GenBank EPB86304]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-87704
-86807
-86782
-88536
-8852
-91779
-642
-701
-71
-725
-645
-957
Rhizopus oryzae [Genebank AER14043]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-118487 -887
-683
-741
-799
-85
-942
-100976
-111223
-119393
-119301
-124532
The best template structure
Tang et al [28] report that Valine plays a key role in stabilizing the accurate orientation of and maintaining the enantioselectivity of the lipase [28] In comparison with our study Mucor circinelloides f circinelloides 1006PhL [EPB86304] modeled lipase showed a substitution of isoleucine (I) to valine (V) in the active site (Figure 2) However Rhizopus oryzae [AER14043] do not have this change and the modeled lipase showed slightly more favorable energy (more negative) for some substrates
Undoubtedly the new findings on the lipasesrsquo structure-function relationships are opening significant exploration ways for applications in several industries For example in industrial bioremediation our findings on functional modification of enzymes will conduct to the rational design of proteins to perhaps improve their substrate specificity enantioselectivity catalytic efficiency and thermostability Lately Zhang et al [29] were shown to improve the performance of Rhizomucor miehei lipase (RML) exhibited on yeast
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
surface in the production of human milk fat substitute (HMFS) [29] They developed an amino acid mutation in the lipase substrate-binding pocket based on protein hydrophobicity improving its activity
They used molecular coupling to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were subs Zhang M XW Yu Y Xu et al Crystal structure of lipase from Rhizopus microsporus var chinensis 2013 (en linea) [httpftpwwpdborgpubpdbvalidation_reportsl34l3w4l3w_full_validationpdf] Acceso 10122017 trates They used molecular docking to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were substrates However although we did not change any residue we obtained higher scores for oleic acid (~ 25 times for our modeled structures) and for tripalmitin ~ 95 for both modeled structures suggesting tremendous future application in bioremediation for the informed lipases here
ConclusionThe molecular docking analysis of 3D models of lipases from
Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases The structural modeling study for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase is reported in this study being Rhizopus oryzae [AER14043] the best model This study highlights fungal lipases and exemplifies its binding to the substrate ie palmitic oleic acid tripalmitin even values more favorable than the template structure However these compounds are potential substrates for these lipases and we suggest that could be evaluated in vitro This is the first study of molecular docking between fatty acids and a tripalmitin of palm oil showing an adequate binding energy accordingly to previous studies with other fungi lipases Future molecular studies will be made for redesigned the models with specifics mutations for perhaps a better interaction with pollutant fatty acids and triglycerides for applications in industry
References1 Mateos JC Rodriacuteguez JA Roussos J Cordova A Abousalham F et al
(2006) Lipase from the thermotolerant fungus Rhizopus homothallicus is more thermostable when produced using solid state fermentation than liquid fermentation procedures Enzyme Microb Technol 39(5)1042ndash1050
2 Cruz-Ramiacuterez MG Rivera-Riacuteos JM Teacutellez-Jurado A Maqueda Gaacutelvez AP Mercado-Flores Y et al (2014) Screening for thermotolerant ligninolytic fungi with laccase lipase and protease activity isolated in Mexico J Environ Biol 35(3) 521-529
3 Okogbenin OB Anisiobi GE Okogbenin EA Ojieabu A (2014) Microbiological assessment and physiochemical parameters of palm oil mill effluent collected in a local mill in Ovia North East area of Edo State Nigeria Herald journal of Microbiology Biotechnology 1(1) 1ndash9
4 Lima ACP Cammarota MC Gutarra MLE (2018) Obtaining filamentous fungi and lipases from sewage treatment plant residue for fat degradation in anaerobic reactors Peer J 6 e5368
5 Efimova E Marjakangas JM Lakaniemi AM Koskinen PE Puhakka JA (2013) Lipid profile characterization of wastewaters from different origins Water Sci Technol 68(11) 2505-2514
6 Mendoza LI (2010) Aislamiento y seleccioacuten de hongos lipoliacuteticos a partir de aceites vegetales de desecho (proveniente de frituras) utilizados en la elaboracioacuten de biodiesel [Thesis] Facultad de Ciencias bioloacutegicas Universidad Nacional Mayor de San Marcos Peru
7 Pruksatrakul T Phoopraintra P Wilairat P Chaiyen P Chantiwas R (2017) Development of a sequential injection-liquid microextraction procedure with GC-FID for analysis of short-chain fatty acids in palm oil mill effluent Talanta 165 612-618
8 Gopinath SC Anbu P Lakshmipriya T Hilda A (2013) Strategies to characterize fungal lipases for applications in medicine and dairy industry Biomed Res Int 2013 154549
9 Singh RK Feller A Roovers M Van Elder D Wauters L et al (2018) Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism RNA 24(8)1080-1092
10 Vasel B Hecht HJ Schmid RD Schomburg D (1993) 3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol J Biotechnol 28(1) 99-115
11 Meng XY Zhang HK Mezei M Cui M (2011) Molecular docking a powerful approach for structure-based drug discovery Curr Comput Aided Drug Des 7(2) 146-157
12 Ericsson DJ Kasrayan A Johansson P Bergfors T Sandstroumlm AG et al (2008) X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation J Mol Biol 376(1) 109-119
13 Nwuche CO Ogbonna JC (2011) Isolation of lipase producing fungi from palm oil mil eflfuent (POME) dumps sites al Nsukka Braz Arch Boil Technol 54(1) 113-116
14 Sigrist CJ Cerutti L de Castro E Langendijk-Genevaux PS Bulliard V et al (2010) PROSITE a protein domain database for functional characterization and annotation Nucleic Acids Res 38 D161ndashD166
15 Singh PK Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions Indian J Microbiol 52(3) 373-380
16 Morris AL MacArthur MW Hutchinson EG Thornton JM (1992) Stereochemical quality of protein structure coordinates Proteins 12(4) 345-364
17 Grosdidier A Zoete V Michielin O (2011) Swiss Dock a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res 39 W270-W277
18 Rehm S Trodler P Pleiss J (2010) Solvent-induced lid opening in lipases a molecular dynamics study Protein Sci 19(11) 2122-2130
19 Borrelli GM Trono D (2015) Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications Int J Mol Sci 16(9) 20774-20840
20 Blow D (1990) Enzymology More of the catalytic triad Nature 343 694-695
21 Juhl PB Trodler P Tyagi S Pleiss J (2009) Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking BMC Struct Biol 9 39
22 Biasini M Bienert S Waterhouse A Arnold K Studer G et al (2014) SWISS-MODEL modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res 42 W252-W258
23 Grosdidier A Zoete V Michielin O (2011) Fast docking using the CHARMM force field with EADock DSS J Comput Chem 32(10) 2149-2159
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
Archives of Organic and Inorganic Chemical Sciences
Assets of Publishing with us
bull Global archiving of articles
bull Immediate unrestricted online access
bull Rigorous Peer Review Process
bull Authors Retain Copyrights
bull Unique DOI for all articles
This work is licensed under CreativeCommons Attribution 40 License
To Submit Your Article Click Here Submit Article
DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
Abstract
Keywords
Introduction
Materials and Methods
Fungi sequence selection and alignment
Homology modeling
Molecular docking
Results and Discussion
Conclusion
References
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Table 1
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
We also used ERRAT (httpnihservermbiuclaedu) which analyses the statistics of non-bonded interactions between different atom types A single output plot was produced by Errat program that gave the value of the error function against position of residues [24] An error value exceeding 99 confidence level indicates poorly modeled regions (Figure 3) Errat analyses also provide an overall quality factor expressed as the percentage of the protein for which the calculated error value falls below the 95 rejection limit Good high resolution structures generally produce values around 95 or higher For lower resolutions (25ndash3Aring) the average overall quality factor is around 91 [24] The overall quality factor assigned for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase models were 883 and 934 respectively
Accordingly with docking study published here it was predicted that modeled lipases have most effective interaction with tripalmitin (binding energy of -957Kcalmol) Docking analysis of Mucor circinelloides f circinelloides 1006PhL modeled lipase with fatty acids and tripalmitin was performed and full fitness energy was recorded The results showed a good interaction more than
one-fatty acids and tripalmiting them (Table 1) We performed the docking with SwissDock with rigid selection We conducted the same procedure with Rhizopus oryzae modelled lipase with these substrates under the same parameters and software and the results were appropriate scores for binding
As a reference a Rhizopus microsporus var Chinensis [EF405962] lipase with PDB ID 4L3W was taken for comparison where accordingly with previous reports [1825-27] We recognized that the triad ArgndashAspndashPro (RDP) is preserved in the lipase responsible for the detection of the molecules tested Our data revealed the above mentioned (VIVTGHSLGG) conserved domain in the lipase from Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] as the main site for lipase activity We also observed that fatty acids and tripalmitin binds into the pocket of the funnel shape active site of both lipases and bonding between the molecules is through hydrogen bond with bond length ~250Aring as previously reported with another ligandenzyme [15] In contrast when we analyzed the result in the lipase the docking score was favorable and fatty acid and tripalmitin molecule were bind given to the protein low fullfitness energy (Table 1)
Table 1 Molecular docking scores for target lipase structures and possible substrates found in palm oil
Source of lipase Ligand Full Fitness (Kcalmol) Estimated ∆G (kJmol)
Rhizopus microspona var Chinensis [PDB 4L3W] ()
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-96678
-105211
-112517
-106898
-114375
-108237
-626
-752
-65
-62
-804
-837
Mucor circinelloides f circinelioides 1006PhL
[GenBank EPB86304]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-87704
-86807
-86782
-88536
-8852
-91779
-642
-701
-71
-725
-645
-957
Rhizopus oryzae [Genebank AER14043]
Linoleic acid [4474613]
Linolenic acid [3870057]
Linolenic acid [3802189]
Oleic acid acid [6845860]
Palmitic acid [6072466]
Tripalmitin [8214701]
-118487 -887
-683
-741
-799
-85
-942
-100976
-111223
-119393
-119301
-124532
The best template structure
Tang et al [28] report that Valine plays a key role in stabilizing the accurate orientation of and maintaining the enantioselectivity of the lipase [28] In comparison with our study Mucor circinelloides f circinelloides 1006PhL [EPB86304] modeled lipase showed a substitution of isoleucine (I) to valine (V) in the active site (Figure 2) However Rhizopus oryzae [AER14043] do not have this change and the modeled lipase showed slightly more favorable energy (more negative) for some substrates
Undoubtedly the new findings on the lipasesrsquo structure-function relationships are opening significant exploration ways for applications in several industries For example in industrial bioremediation our findings on functional modification of enzymes will conduct to the rational design of proteins to perhaps improve their substrate specificity enantioselectivity catalytic efficiency and thermostability Lately Zhang et al [29] were shown to improve the performance of Rhizomucor miehei lipase (RML) exhibited on yeast
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
surface in the production of human milk fat substitute (HMFS) [29] They developed an amino acid mutation in the lipase substrate-binding pocket based on protein hydrophobicity improving its activity
They used molecular coupling to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were subs Zhang M XW Yu Y Xu et al Crystal structure of lipase from Rhizopus microsporus var chinensis 2013 (en linea) [httpftpwwpdborgpubpdbvalidation_reportsl34l3w4l3w_full_validationpdf] Acceso 10122017 trates They used molecular docking to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were substrates However although we did not change any residue we obtained higher scores for oleic acid (~ 25 times for our modeled structures) and for tripalmitin ~ 95 for both modeled structures suggesting tremendous future application in bioremediation for the informed lipases here
ConclusionThe molecular docking analysis of 3D models of lipases from
Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases The structural modeling study for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase is reported in this study being Rhizopus oryzae [AER14043] the best model This study highlights fungal lipases and exemplifies its binding to the substrate ie palmitic oleic acid tripalmitin even values more favorable than the template structure However these compounds are potential substrates for these lipases and we suggest that could be evaluated in vitro This is the first study of molecular docking between fatty acids and a tripalmitin of palm oil showing an adequate binding energy accordingly to previous studies with other fungi lipases Future molecular studies will be made for redesigned the models with specifics mutations for perhaps a better interaction with pollutant fatty acids and triglycerides for applications in industry
References1 Mateos JC Rodriacuteguez JA Roussos J Cordova A Abousalham F et al
(2006) Lipase from the thermotolerant fungus Rhizopus homothallicus is more thermostable when produced using solid state fermentation than liquid fermentation procedures Enzyme Microb Technol 39(5)1042ndash1050
2 Cruz-Ramiacuterez MG Rivera-Riacuteos JM Teacutellez-Jurado A Maqueda Gaacutelvez AP Mercado-Flores Y et al (2014) Screening for thermotolerant ligninolytic fungi with laccase lipase and protease activity isolated in Mexico J Environ Biol 35(3) 521-529
3 Okogbenin OB Anisiobi GE Okogbenin EA Ojieabu A (2014) Microbiological assessment and physiochemical parameters of palm oil mill effluent collected in a local mill in Ovia North East area of Edo State Nigeria Herald journal of Microbiology Biotechnology 1(1) 1ndash9
4 Lima ACP Cammarota MC Gutarra MLE (2018) Obtaining filamentous fungi and lipases from sewage treatment plant residue for fat degradation in anaerobic reactors Peer J 6 e5368
5 Efimova E Marjakangas JM Lakaniemi AM Koskinen PE Puhakka JA (2013) Lipid profile characterization of wastewaters from different origins Water Sci Technol 68(11) 2505-2514
6 Mendoza LI (2010) Aislamiento y seleccioacuten de hongos lipoliacuteticos a partir de aceites vegetales de desecho (proveniente de frituras) utilizados en la elaboracioacuten de biodiesel [Thesis] Facultad de Ciencias bioloacutegicas Universidad Nacional Mayor de San Marcos Peru
7 Pruksatrakul T Phoopraintra P Wilairat P Chaiyen P Chantiwas R (2017) Development of a sequential injection-liquid microextraction procedure with GC-FID for analysis of short-chain fatty acids in palm oil mill effluent Talanta 165 612-618
8 Gopinath SC Anbu P Lakshmipriya T Hilda A (2013) Strategies to characterize fungal lipases for applications in medicine and dairy industry Biomed Res Int 2013 154549
9 Singh RK Feller A Roovers M Van Elder D Wauters L et al (2018) Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism RNA 24(8)1080-1092
10 Vasel B Hecht HJ Schmid RD Schomburg D (1993) 3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol J Biotechnol 28(1) 99-115
11 Meng XY Zhang HK Mezei M Cui M (2011) Molecular docking a powerful approach for structure-based drug discovery Curr Comput Aided Drug Des 7(2) 146-157
12 Ericsson DJ Kasrayan A Johansson P Bergfors T Sandstroumlm AG et al (2008) X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation J Mol Biol 376(1) 109-119
13 Nwuche CO Ogbonna JC (2011) Isolation of lipase producing fungi from palm oil mil eflfuent (POME) dumps sites al Nsukka Braz Arch Boil Technol 54(1) 113-116
14 Sigrist CJ Cerutti L de Castro E Langendijk-Genevaux PS Bulliard V et al (2010) PROSITE a protein domain database for functional characterization and annotation Nucleic Acids Res 38 D161ndashD166
15 Singh PK Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions Indian J Microbiol 52(3) 373-380
16 Morris AL MacArthur MW Hutchinson EG Thornton JM (1992) Stereochemical quality of protein structure coordinates Proteins 12(4) 345-364
17 Grosdidier A Zoete V Michielin O (2011) Swiss Dock a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res 39 W270-W277
18 Rehm S Trodler P Pleiss J (2010) Solvent-induced lid opening in lipases a molecular dynamics study Protein Sci 19(11) 2122-2130
19 Borrelli GM Trono D (2015) Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications Int J Mol Sci 16(9) 20774-20840
20 Blow D (1990) Enzymology More of the catalytic triad Nature 343 694-695
21 Juhl PB Trodler P Tyagi S Pleiss J (2009) Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking BMC Struct Biol 9 39
22 Biasini M Bienert S Waterhouse A Arnold K Studer G et al (2014) SWISS-MODEL modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res 42 W252-W258
23 Grosdidier A Zoete V Michielin O (2011) Fast docking using the CHARMM force field with EADock DSS J Comput Chem 32(10) 2149-2159
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
Archives of Organic and Inorganic Chemical Sciences
Assets of Publishing with us
bull Global archiving of articles
bull Immediate unrestricted online access
bull Rigorous Peer Review Process
bull Authors Retain Copyrights
bull Unique DOI for all articles
This work is licensed under CreativeCommons Attribution 40 License
To Submit Your Article Click Here Submit Article
DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
Abstract
Keywords
Introduction
Materials and Methods
Fungi sequence selection and alignment
Homology modeling
Molecular docking
Results and Discussion
Conclusion
References
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Table 1
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
surface in the production of human milk fat substitute (HMFS) [29] They developed an amino acid mutation in the lipase substrate-binding pocket based on protein hydrophobicity improving its activity
They used molecular coupling to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were subs Zhang M XW Yu Y Xu et al Crystal structure of lipase from Rhizopus microsporus var chinensis 2013 (en linea) [httpftpwwpdborgpubpdbvalidation_reportsl34l3w4l3w_full_validationpdf] Acceso 10122017 trates They used molecular docking to calculate the binding energy between lipase and substrates finding that one mutant had significantly lower energy when oleic acid (-397KJmol) and tripalmitin (755KJmol decrease) were substrates However although we did not change any residue we obtained higher scores for oleic acid (~ 25 times for our modeled structures) and for tripalmitin ~ 95 for both modeled structures suggesting tremendous future application in bioremediation for the informed lipases here
ConclusionThe molecular docking analysis of 3D models of lipases from
Mucor circinelloides f circinelloides 1006PhL [EF405962] and Rhizopus oryzae [AER14043] suggest that pollutant fatty acids can bind to fungi lipases The structural modeling study for Mucor circinelloides f circinelloides 1006PhL [EPB86304] and Rhizopus oryzae [AER14043] lipase is reported in this study being Rhizopus oryzae [AER14043] the best model This study highlights fungal lipases and exemplifies its binding to the substrate ie palmitic oleic acid tripalmitin even values more favorable than the template structure However these compounds are potential substrates for these lipases and we suggest that could be evaluated in vitro This is the first study of molecular docking between fatty acids and a tripalmitin of palm oil showing an adequate binding energy accordingly to previous studies with other fungi lipases Future molecular studies will be made for redesigned the models with specifics mutations for perhaps a better interaction with pollutant fatty acids and triglycerides for applications in industry
References1 Mateos JC Rodriacuteguez JA Roussos J Cordova A Abousalham F et al
(2006) Lipase from the thermotolerant fungus Rhizopus homothallicus is more thermostable when produced using solid state fermentation than liquid fermentation procedures Enzyme Microb Technol 39(5)1042ndash1050
2 Cruz-Ramiacuterez MG Rivera-Riacuteos JM Teacutellez-Jurado A Maqueda Gaacutelvez AP Mercado-Flores Y et al (2014) Screening for thermotolerant ligninolytic fungi with laccase lipase and protease activity isolated in Mexico J Environ Biol 35(3) 521-529
3 Okogbenin OB Anisiobi GE Okogbenin EA Ojieabu A (2014) Microbiological assessment and physiochemical parameters of palm oil mill effluent collected in a local mill in Ovia North East area of Edo State Nigeria Herald journal of Microbiology Biotechnology 1(1) 1ndash9
4 Lima ACP Cammarota MC Gutarra MLE (2018) Obtaining filamentous fungi and lipases from sewage treatment plant residue for fat degradation in anaerobic reactors Peer J 6 e5368
5 Efimova E Marjakangas JM Lakaniemi AM Koskinen PE Puhakka JA (2013) Lipid profile characterization of wastewaters from different origins Water Sci Technol 68(11) 2505-2514
6 Mendoza LI (2010) Aislamiento y seleccioacuten de hongos lipoliacuteticos a partir de aceites vegetales de desecho (proveniente de frituras) utilizados en la elaboracioacuten de biodiesel [Thesis] Facultad de Ciencias bioloacutegicas Universidad Nacional Mayor de San Marcos Peru
7 Pruksatrakul T Phoopraintra P Wilairat P Chaiyen P Chantiwas R (2017) Development of a sequential injection-liquid microextraction procedure with GC-FID for analysis of short-chain fatty acids in palm oil mill effluent Talanta 165 612-618
8 Gopinath SC Anbu P Lakshmipriya T Hilda A (2013) Strategies to characterize fungal lipases for applications in medicine and dairy industry Biomed Res Int 2013 154549
9 Singh RK Feller A Roovers M Van Elder D Wauters L et al (2018) Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism RNA 24(8)1080-1092
10 Vasel B Hecht HJ Schmid RD Schomburg D (1993) 3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol J Biotechnol 28(1) 99-115
11 Meng XY Zhang HK Mezei M Cui M (2011) Molecular docking a powerful approach for structure-based drug discovery Curr Comput Aided Drug Des 7(2) 146-157
12 Ericsson DJ Kasrayan A Johansson P Bergfors T Sandstroumlm AG et al (2008) X-ray structure of Candida antarctica lipase A shows a novel lid structure and a likely mode of interfacial activation J Mol Biol 376(1) 109-119
13 Nwuche CO Ogbonna JC (2011) Isolation of lipase producing fungi from palm oil mil eflfuent (POME) dumps sites al Nsukka Braz Arch Boil Technol 54(1) 113-116
14 Sigrist CJ Cerutti L de Castro E Langendijk-Genevaux PS Bulliard V et al (2010) PROSITE a protein domain database for functional characterization and annotation Nucleic Acids Res 38 D161ndashD166
15 Singh PK Shukla P (2012) Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions Indian J Microbiol 52(3) 373-380
16 Morris AL MacArthur MW Hutchinson EG Thornton JM (1992) Stereochemical quality of protein structure coordinates Proteins 12(4) 345-364
17 Grosdidier A Zoete V Michielin O (2011) Swiss Dock a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res 39 W270-W277
18 Rehm S Trodler P Pleiss J (2010) Solvent-induced lid opening in lipases a molecular dynamics study Protein Sci 19(11) 2122-2130
19 Borrelli GM Trono D (2015) Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications Int J Mol Sci 16(9) 20774-20840
20 Blow D (1990) Enzymology More of the catalytic triad Nature 343 694-695
21 Juhl PB Trodler P Tyagi S Pleiss J (2009) Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking BMC Struct Biol 9 39
22 Biasini M Bienert S Waterhouse A Arnold K Studer G et al (2014) SWISS-MODEL modelling protein tertiary and quaternary structure using evolutionary information Nucleic Acids Res 42 W252-W258
23 Grosdidier A Zoete V Michielin O (2011) Fast docking using the CHARMM force field with EADock DSS J Comput Chem 32(10) 2149-2159
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
Archives of Organic and Inorganic Chemical Sciences
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DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
Abstract
Keywords
Introduction
Materials and Methods
Fungi sequence selection and alignment
Homology modeling
Molecular docking
Results and Discussion
Conclusion
References
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Table 1
Citation J Moya-Salazar J Veacutertiz-Osores S Jibaja R Acevedo-Espinola R Rupa et al Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil Effluent Arc Org Inorg Chem Sci 4(2)- 2019 AOICSMSID000183 DOI 1032474AOICS201904000183
24 Sehgal SA Tahir RA Mirza AH (2018) Quick Guideline for Computational Drug Design Bentham eBooks Netherlands
25 Zhang JH Jiang YY Lin Y Sun YF Zheng SP et al (2013) Structure-guided modification of Rhizomucor miehei lipase for production of structured lipids PLoS One 8(7) e67892
26 Yang S Qin Z Duan X Yan Q Jiang Z (2015) Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei J Lipids Res 56(8) 1616-1624
27 Zan X Tang X Chu L Zhao L Chen H et al (2016) Lipase genes in Mucor circinelloides identification sub-cellular location phylogenetic analysis and expression profiling during growth and lipid accumulation J Ind Microbiol Biotechnol 43(10)1467-1480
28 Tang L Su M Chi L Zhang J Zhang H et al (2014) Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase Biotechnol Lett 36(3) 633-639
29 Zhang M Yu XW Xu Y Huang CH Guo RT (2013) Crystal structure of lipase from Rhizopus microsporus var chinensis
Archives of Organic and Inorganic Chemical Sciences
Assets of Publishing with us
bull Global archiving of articles
bull Immediate unrestricted online access
bull Rigorous Peer Review Process
bull Authors Retain Copyrights
bull Unique DOI for all articles
This work is licensed under CreativeCommons Attribution 40 License
To Submit Your Article Click Here Submit Article
DOI 1032474AOICS201904000183
Fungi Lipases Homology Modeling and Molecular Docking with Fatty Acids and Tripalmitin of Palm Oil E
